I would say that Bayesians are the ones who are actually addressing the problems that most frequentists only think that they are...which I suppose is the same thing as Bill Jefferys' comment:

Since my background and training are in the physical sciences, I've noticed that all but the most sophisticated of my colleagues (that is, those that have learned enough statistics to be dangerous :0), think that a confidence interval is a credible interval. Which is natural, if mistaken.

Of course the IPCC proved that these entities are the same, back in the TAR...

It appears to have been written a little later than the other comments, although overlapping such that Kirk-Davidoff didn't seem to know of our work before the initial submission (it is useful that ACP/ACPD has the old manuscript and reviews on line so the full history can be checked).

The comment is a more thorough investigation than we or Knutti et al could fit into the tight page limit of JGR comments, but I don't think there is anything materially different. As well as looking at the IPCC database (and concluding that the analysis method does not usefully indicate the equilibrium sensitivity of these models) Kirk-Davidoff investigated a slightly more complex model than the simple energy balance we used, and found that the method was useless for that too (or to be precise, in principle it would work given a long enough time series of observations, that is not available for the real climate system). I presume the reasons are much the same for the more complex model as for the simpler model we analysed, but there is probably no easy analytical solution in the more complex example.

There is no response from Schwarz in the review process (or as a separate paper, which I believe is possible through the ACP/ACPD system). I hope (and expect) that the editor, and indeed the author, contacted him about it. Of course he has already basically admitted it is wrong in his reply to us.

Odd, therefore, that the Schwartz stuff continues to get pimped on the Wikipedia page...

Wednesday, September 23, 2009

Clue 2:The manual for the truck boasts than it can pull a boat, but then our Nissan Micra used to do that and it could also do 50mpg with a tandem on the roof. Happily we already have mud going up to the door handles. Today we head out into the wilds. I wonder if there will be more or less internet there.

Sunday, September 20, 2009

The survey doesn't make clear how the authors were selected, which could make a difference if more prolific authors had a better chance of being picked. Or, indeed, if those who had suffered had actually left science and were unreachable. But still, there isn't much surprise there. Peer review works reasonably well on the whole, it can't always stop the misguided if they are determined enough but it can slow them down and on the whole I'm sure it improves the quality of the final papers, thus providing a benefit to the community. I have commented before that I like the idea of the EGU system where the review process is public but reviewers can remain anonymous. This is, however, only a tweak to the overall system.

IMO the more interesting debate in publishing relates more to the open access vs paywall question. For Climatic Change, I had the option of paying $3000 for my recent paper to be open access, so that's a benchmark for the value of the effort that authors, reviewers, and editors are donating to the profits of private businesses. (I know, the supporting editorial services are not completely free: the EGU manages it for about €25 per page.)

Saturday, September 19, 2009

The weird thing is that this is not 2 photos stitched together. Sometimes temples invest their year-end extra-budget in a new staircase. Usually the old stairs are then cordoned off and revered, but not so at Zuisenji.

Friday, September 18, 2009

Last day of school before the holidays! And I bought some photo-apps for my iphone to play with on the plane.

Meanwhile we trytocapturethequintessenceofthe red higanbana, but fail because the amazing thing about them is the way the green stem shoots from bare ground and full bloom follows 2 days later. The leaves follow and feed the bulb over the winter. If you had a pet higanbana in your garden then a time lapse movie could be a lot of fun.

Mind you, the suggested one day conversion of parking spaces seems a bit...weak. My own permanent PARK(ing) space can be seen here, in an old picture that dates back to before global warming really took hold (otherwise known as winter a few years back):

The viewpoint doesn't really show it off to best advantage - there are more plants off-screen to the right - but I can hardly do a better job now it's dark out. Anyway, being privately owned, I'm not sure if it counts, but it should. I do pay ¥25000 per month for it, but that is really a fiddle to get round JAMSTEC's silly rules over house rentals rather than a real parking space rental.

As an aside, I don't think there is actually that much need for guerrilla gardening in Japan. The climate being what it is, any unused space is reclaimed very rapidly (eg spot the greenness peeking though here). Also, people here are pretty keen on gardening and like to put pots out wherever there is a few inches of space - in fact that same residential road where the scrap metal dump is, is also lined with flowers, tomatoes, and chilli plants all through the summer. The problem is in really in preventing people from paving, repaving, and expanding over undeveloped areas at an ever-increasing rate.

Apparently it's going to be shown in a sealed-off area, hidden from public view by tarpaulins:

No, I jest. The real solution is much more Japanese. The film is being shown, but no-one is going to be told when or where (the decision was "too late" to include it in the printed program and press information, there is currently no mention of it on the official web site), and you have to apply three months in advance for tickets:

PROSSER: But Mr. Dent, the plans have been available in the local planning office for the last nine months!

ARTHUR: Yes, well, as soon as I heard, I went straight round to see them. You hadn’t gone out of your way to call attention to them, had you? I mean, like actually telling anybody.

PROSSER: The plans were on display—

ARTHUR: On display? I had to go down to the cellar to find them!

PROSSER: That’s the display department!

ARTHUR: With a flashlight.

PROSSER: The lights had probably gone out.

ARTHUR: So had the stairs.

PROSSER: But you found the notice, didn’t you?

ARTHUR: Yes, I did. It was "on display" in the bottom of a locked filing cabinet stuck in a disused lavatory with a sign on the door saying, "Beware of the Leopard."

Even Japanese officials admit that the dolphin meat is so contaminated by mercury that it should be classified as "toxic waste", but of course in the country that invented Minamata disease it's part of longstanding tradition to force-feed such stuff to schoolchildren.

Unfortunately they don't get much scarier than the gejigeji, so it might be safe to read this blog with your eyes open for a while ... unless we meet a mukade (Although I think they are less horrifying to look at - the terror stems more from the fact they are actually dangerous).

These spider lilies are spiders in name only. They are also called equinox lilies (higanbana in Japanese), and they are a good week early. The red variety is very common by the roadside, but Zuisenji, our local temple, seems to have gone a bit overboard on white for this equinox.

Wednesday, September 16, 2009

Should it actually be "James' scary blog"? All I can say to Martin is he'd best have his geologists hammer at the ready, and let's hope it's good and heavy. Hey, perhaps that leaf is really really small and not at all a leaf from a giant bamboo? We can only hope.

Despite the ease with which they fill the frame, it is quite hard to photograph the gejigeji because they are most active at night. James chased this one with the sieve all night , but it eluded him, only to be found waiting patiently by the door in the morning. Managed to snap a few shots after we chased it out of the door, as it blinked in the morning light.

Tuesday, September 15, 2009

At this time of year these camp all round our house awaiting tasty boyfriends. The even better ones, however, spin up a massive web made from fishing line strength silk across the mountain path at dusk and capture tandem mountain bikers heading home.

Monday, September 14, 2009

The latest More or Less has Andrew Gelman being politely dismissive of some extremely dodgy work on sex ratios that he has blogged about a number of times (and written some papers).

There was also a bit about climate prediction. Mojib Latif has got himself in the news recently with some comments about his prediction of short-term cooling which of course the denialosphere loved. He's part of the Keenlyside et al team, but I'm far as I'm aware there is no new research behind his statements which were made at a big political meeting. I don't think anyone believed the Keenlyside et al work when it appeared, and the Pope (ha) put the boot in ever so gently, describing the work the Hadley Centre had done (that I mentioned some time ago) to show that the method that Keenlyside et al used doesn't work.

Oh yes, as for the vague allusion to me, if the promised El Nino lasts over the winter then I should have a good chance of collecting on the bet I made on More or Less last year. Not that it's a sure thing or anything. I'm in with a reasonably good chance here too - if the current melt continues for another week I'll be in the money...

James has previously waxed lyrical on the virtues of the church of St Arbuck, where he regularly attends the early morning service on Sundays. This is his favourite one, which can be found a few minutes walk from the west (non-tourist!) side of Kamakura station.

Friday, September 11, 2009

Forgot to mention it, but I put some more pics of our recent mountain trip up on a web page. So if anyone wants to see what our weekends look like, click here.

The day after we returned, a typhoon came through and the temperature never bounced back. So that wasn't much of a summer. Not that it's unpleasant, or anything like that - quite the reverse, we are having some comfortable shorts and t-shirt weather for a week or two as we start the precipitous descent into what passes for winter here.

Just one of the dangers facing wee Trevorina the praying mantis as she seeks out tasty boyfriends out in the wilds of Kamakura. The largest hornet in the world may not look like much in this photo taken from some distance away, but they're the size of a pepper pot, sound like a helicopter and after a face-off from 10 feet or so one is left with a freaky impression of big black eyes. There seem to be many more than usual around this year. This one was drinking from the puddles in Hase Dera.

Thursday, September 10, 2009

McDonalds is doing an ad campaign featuring a dorky American who can't speak proper Japanese but comes to visit because of the wonderful Japanesified McDonalds food (as an aside, the thought of people actually coming here specifically due to the bastardised "western-style" crap that gets served in restaurants is pretty funny - mayonnaise and potato pizza, anyone? How about minestrone soup and salad for your "western-style" breakfast?) The usual suspects are up in arms about the stereotyping etc, but that's another story.

Anyway, he starts out as a reasonably normal-sized character (unthreateningly short, judging from the cardboard cutout we found in Akihabara recently):

After a few weeks of his favourite burger, the Tamago Double Mac (double mac with egg), he's settled in nicely:

Wednesday, September 09, 2009

Lots of fishies at Hase Dera, which is a short walk from the Daibutsu (and no where near Gundam) . However, despite its many attractions, wouldn't really recommend Hase for a visit right now since its main feature, a gold coloured wooden statue which is the biggest, best, something in Japan (not even in the top ten it's so good), is mostly hidden from view behind scaffolding.

One of the pleasures of living in Japan is the ease of living a car-free life. Not that it's impossible anywhere, but here it is positively convenient, and the savings on taxes and car maintenance fees are substantial.

So, after 8 years of not even wanting to drive, a couple of days ago I went and got a licence. The motivation was actually the chance discovery that the rental fee in the USA (where I'm going on holiday) is much cheaper for Japanese residents than UK ones, as the former get the loss damage waiver insurance thrown in for free. I have no idea why this is the case, but am not going to complain. Although I already am a Japanese resident, my licence is a UK one and a check with Avis head office confirmed my fears that this would be a problem. Since there's an automatic swap system between UK and Japanese licences I thought I might as well just go and do it.

I'm writing this post partly for the benefit of future applicants, so I should ensure that Google indexes it prominently as a description of how to exchange a UK driving licence for a Japanese driving licence.

It only took me a day from start to finish, but the process was a little more fraught than I had anticipated. First I went to the local JAF office (Japanese version of AA) to get an official translation of my UK licence. This went very smoothly and only took 30 minutes, barely long enough for me to have coffee and pancakes in the Denny's opposite.

I was in the Kanagawa licence office before 11am. In fact I was so early that I had to make my own sign-up sheet to make sure of my place in the queue for the 1-1:30 time slot. They were limiting the number of applications to 12 people that day. My local office in Kanagawa is also open 8:30-9:00am for anyone who has got the translation ahead of time (that can be done by post, it takes about a week but I didn't have time for that). I had a good book and was well prepared for waiting.

Eventually 1:00 rolled around and they opened up reception. I think there were only 12 gaijin applicants in total, some of who only came in after 1:30 - they were still processing people so had not shut the window.

The first problem was that in line with all the advice I had received, I had brought my current and previous (when I came to Japan) passport, but they also wanted to see the one that I held when I first got my driving licence which was more than 20 years ago! Thinking quickly, I told them I hadn't had a passport at that time (well it could have been true). This only got them asking about my first trip abroad, how old I'd been and where I had gone...I was bluffing pretty badly here, trying to work out what the first trip on my previous passport might have been (back in 1995 or 1996!), while explaining that it was all too long ago to remember, but they either believed me or just took took pity on me and took my documents and told me to sit down and wait. For the record, I now realise that my first overseas trip was age 3, on my parents' passport, but I didn't even remember that under duress and thinking in Japanese. Probably just as well!

Then half an hour later they called me up again and started asking again about my foreign trips and in particular my comings and goings while living in Japan. Apart from the fact that I simply couldn't remember in detail, my confusion of saigo and saisho (last/first) added to the confusion. Eventually I managed to persuade them to bring my passport over which had the relevant stamps in,and I pointed to my last trip...and then they were all confused because the passport showed that I had registered to use the automatic gate system at immigration but had a manual stamp. IME the automatic gate is usually either non-functional or has no benefits anyway, as the normal queue is quicker, so although I registered once when I had spare time at the airport, I've not used it since. I wonder if the guy was on secondment from immigration or something, and had visions of being dragged away in handcuffs and deported. Incidentally, there is nothing remotely controversial or dodgy about my visa status during my time here, so I really have no idea what they so worked up about.

Lots of other people also had to deal with various queries about dates on licences and passports. It seems they have some pedantic bureaucratic requirements but I didn't see anyone actually getting sent away so maybe it's more a matter of working out what to put on the forms than determining the legitimacy of the application. There is some requirement to have lived in the country where the licence was issued for a certain period of time, but whether that time has to be immediately adjacent to the date of issue is not entirely clear.

After that, it was suddenly all plain sailing, and they were very helpful and cooperative. The only testing as such was a trivial eye test and some routine questions about health, which were translated into English. I guess I was the only one of the batch of foreigners to actually get a licence that day, as I got mine just before 4:30 and they seemed to be winding down. I think most of the others had some sort of test to do too, either written or driving.

A lot of the others had come with a Japanese friend, but the form filling and questioning was not really very hard and the staff did their best to speak easily and use English. Of course it might have been another matter if I'd had to do a test, but for what I had to do, a smattering of conversational Japanese would be fine. It would certainly be daunting to attempt it fresh off the boat though.

Although at the time it seemed like an arduous and unpleasant experience, it was actually only 7h30 from start to finish, including getting the translation, and at the end I had a real shiny new freshly printed licence card in my hand. I doubt there are many other countries in the world where that would happen, especially for a virtually mute and illiterate foreigner. Japanese bureaucracy isn't always that bad. The American man behind in the queue me spent the entire time gurning to his Japanese wife about how awful the process was, but I bet he doesn't work for JAMSTEC. All I needed was my passports, UK licence, one passport-sized photo, gaijin card, and ¥7500 in total for the various fees.

Tuesday, September 08, 2009

This is the Buddhist equivalent of Shift-A in Google Reader (mark all as read). One revolution of the rotating bookshelves containing the Buddhist sutras confers the same merit as actually reading them. There really ought to be something equivalent for the IPCC report.

Sunday, September 06, 2009

An email about travel to the AGU meeting in San Francisco was sent round at work recently. I've rewritten for clarity, but the meaning was the same in the original:

Flights from San Francisco to Narita on Dec. 19 [the day after the meeting ends] are going to be busy. We have already booked some seats, so please ask soon if you need one. Please do not delay your departure date to the 20th even if you can not find a seat on the 19th. JAMSTEC rules prohibit this.

I wonder if they will refund the cost of water wings?

(The "official" solution to the conundrum is to return on the 18th, irrespective of whether you are scheduled to give a presentation that day, which of course people don't even know at this time...note that all flights leave in the morning, so there is no question of dashing to the airport straight from the session.)

Science has a fairly vacuous article (How Will Science Fare?) about the forthcoming science budget negotiations in Japan. Not that I'm really blaming them, I'm sure they've got pages to fill and no-one seems to know either what the DPJ will try to do, nor whether they will actually be able to do it given the iron grip that bureaucrats have on the country.

In an annual rite of summer, the education ministry's budget requests are trimmed by advisory bodies, politicians, and the powerful finance ministry. This year, there is a new twist: The newly elected Democratic Party now has responsibility for finalizing the budget—and no one knows how R&D will fare.

The Democratic Party's platform keys in on the importance of research. But the party also promised to cut wasteful governmental spending, without being specific, and party politicians have called for reining in bureaucracy.

There's a specific goal of becoming a low-carbon economy, but it's not clear to me that this really needs a lot of climate science.

I saw another comment of potential interest, regarding proposals to ban contract work:

Our institute is built on short-term contract employment, so it's possible that this could lead to a bit of a shake-up. However it may be solely focussed on the truly short-term (daily/monthly) hiring of cheap labour in manufacturing industry, so we'll have to wait and see what this really means. By the time anything reaches us it may well be unrecognisable in terms of the official policy anyway. For example, a govt science committee recently recommended the introduction of more tenure-track positions, which JAMSTEC reinterpreted to mean hiring more junior post-docs on contracts...

Thursday, September 03, 2009

Why is it OK to feed an ugly brown hoppy insect to your mantis but not a beautiful orange butterfly? I think we will have to release Trevorina soon, and keep pet crickets instead. Having said that, James' herb garden is much healthier since all the grasshoppers got eaten by our fully organic pest control system. Trevorina has been an adult for a while and must be nearly ready to start making next year's mantises. Where to release her? While finding grassland at edge of the forest is easy, finding grassland that wont be cut before the eggs hatch next year is more difficult.

I thought Myles was vehemently opposed to scientists making any statements in public that had not been peer-reviewed, but maybe he was outvoted by his co-authors. Anyway, he now seems comfortable in criticising the approach of Frame et al 2005 as "arbitrary", and says that "Setting the prior to a constant [meaning uniform] is not an option". Shame he didn't agree with us three and a half years ago - or even in 2007 when he was still promoting uniform priors - but better late than never. I'm not going to gloat - seriously, I'd be glad if the whole sorry mess was finished with.

Unfortunately, it is not quite so clear that the whole sorry mess really is finally finished with. Although they now state that uniform priors are unacceptable, they don't actually go the whole hog and accept that subjective priors are unavoidable, but instead present another cook-book solution - the Jeffreys' prior! Apparently, this approach now provides an "objective" solution that eliminates the "arbitrariness". Of course Frame et al made exactly the same claims back in 2005, right down to the choice of words. Plus ça change...but this time, I suppose they really mean it :-)

As yet, it seems like no-one has actually calculated a Jeffreys' prior in any such complex case, and this paper suggests a bunch of simplifications to make it at all tractable - including the assumption that the data are independent, which of course is something Allen was quick to criticise whenever I dared to suggest it. Probably the tablets of stone are being engraved as I type and the solution will be breathlessly announced via the pages of Nature shortly.

As I said in an email recently (and demonstrated in our paper), a more constructive step IMO may not be to attempt to prescribe the one true prior that everyone one must use, but rather to check carefully what any particular prior actually means, in terms of the decisions it supports. If the prior actually reduces to "OMG we're all going to die!!11!!eleventy!1!" (as a uniform prior on S does) then we should not be overly surprised if the posterior remains somewhat alarming, even when updated with whatever data we happen to have. But so far researchers seem curiously reluctant to present their prior predictive probabilities in that way.

Tuesday, September 01, 2009

The Tokyo Daibutsu may vanquish the forces of evil on a regular basis (or whatever it did, I'm happy to say I've never seen the program) but it was brought to its knees by yesterday's wimpy little typhoon:

Rumour has it that the Kamakura Gundam is still sitting comfortably, having seen much worse in his 750+ years...including regular typhoons, a notable tsunami that destroyed his house, and major earthquakes roughly every 80 years.

As I hinted at in a previous post, I've some news regarding the uniform prior stuff. I briefly mentioned a manuscript some time ago, which at that time had only just been submitted to Climatc Change (prompted in part by Myles Allen's snarky comments, I must remember to thank him if we ever meet). Well, eventually the reviews arrived, which were basically favourable, and the paper was accepted after a few minor revisions. The final version is here, and I've pasted the abstract at the bottom of this post.

The content is essentially the same as the various rejected manuscripts we've tried to publish (eg here and here): that is, a uniform prior for climate sensitivity certainly does not represent "ignorance" and moreover is a useless convention that has no place in research that aims to be policy-relevant. With a more sensible prior (even a rather pessimistic one) there seems to be no plausible way of creating the high tails that have been a feature of most published estimates. I'm sure you can join the dots to the recent IPCC report, and the research it leant on so heavily on this topic, yourself.

Obviously there's the possibility of learning lessons about how to present criticism of existing research. This topic came up again only recently, and it's obvious that there are pros and cons to the different approaches. I saw that Gavin Schmidt published a couple of papers recently (1, 2) that were comments without being comments, in that they basically focussed on weaknesses in previous papers without explicitly being presented as "Comment on" with accompanying reply. However, I'd certainly have liked to see Allen and Frame's attempted defence appear in public, as I believe its weakness goes a long way to making our case for us. As things stand, a 3rd party reader will see our point of view but may reasonably wonder whether there are strong arguments for the other side - but don't worry, there aren't :-)

On the other hand, there is no question that the final manuscript is improved by being able to go beyond the direct remit of merely criticising a single specific paper. In particular, the simple economic analysis that we tacked on converts what might be a rather abstruse and mathematical discussion of probability into a direct statement of financial implications (albeit a rather simplified one).

I think one particular difficulty we faced with either approach is that we were not able to present a simple glib solution to the choice of prior, as we do not believe that such a solution exists. The prior that we do use (Cauchy-type) is fairly pathological and hard to recommend. In particular, if one adopts an economic analysis based on a convex utility function such as Weitzman suggests then it's not going to give sensible answers as the expected loss will always be infinite (even for 1ppm extra of CO2, essentially irrespective of what observations we make). However, that is an argument primarily in the field of economics and even philosophy, and not particularly critical as far as the climate science itself goes. The take-home message is that even with such a horrible prior, the posterior is nothing like as scary as those presented in many recent papers.

Of course, this result does bring with it my first loss in climate-related bets. Jules had wagered £500 with me that this previous paper would, if rewritten appropriately, be accepted in Climatic Change, and I was pessimistic enough to take her on. I'm quite happy to lose that bet! (I'd be happy to lose the one on 20 year trends too, if it meant that global warming was a much smaller problem than it now appears.) I suppose I should revise my opinions of the peer review system upwards a little. Apart from the extremely long delay - well over a year so far, and it's not published yet - the process worked well this time, with sensible reviewers making a number of helpful suggestions.

Anyway, here's the abstract:

The equilibrium climate response to anthropogenic forcing has long been one of the dominant, and therefore most intensively studied uncertainties, in predicting future climate change. As a result, many probabilistic estimates of the climate sensitivity (S) have been presented. In recent years, most of them have assigned signiﬁcant probability to extremely high sensitivity, such as P(S > 6C) > 5%.

In this paper, we investigate some of the assumptions underlying these estimates. We show that the popular choice of a uniform prior has unacceptable properties and cannot be reasonably considered to generate meaningful and usable results. When instead reasonable assumptions are made, much greater conﬁdence in a moderate value for S is easily justified, with an upper 95% probability limit for S easily shown to lie close to 4C, and certainly well below 6C. These results also impact strongly on projected economic losses due to climate change.

A week ago, when we visited Gundam it was so hot that the buildings were melting, as you can see in this photo taken in Geektown (Akihabara). It could be that another trip to Akihabara may be forthcoming soon since, on Sunday, for the first time ever (I was brought up proper, to not drink or gamble) I won a massive bet, of 500 UKP!!!! I wonder if James will explain all abut it on his empty blog.

I'm surprised to see FRCGC advertising for new staff, as it closed in April :-) I suppose updating the web site is not a major priority, but we are now officially called RIGC. Anyway, one thing I can promise the successful applicants is an interesting time, at least in some respects...